Changeset 7635

Timestamp:

Mar 11, 2019, 11:01:10 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #2136: Remove support for spot images

Removed spot-image related functionality from the web client.

Location:

trunk

Files:

• config/dist/web.xml (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/servlet/ViewSpotImage.java (deleted)
• www/views/experiments/explorer/view/view.jsp (modified) (2 diffs)
• www/views/rawbioassays/bioassays.js (modified) (2 diffs)
• www/views/rawbioassays/edit_spotimages.jsp (deleted)
• www/views/rawbioassays/index.jsp (modified) (2 diffs)
• www/views/rawbioassays/rawdata/list_rawdata.jsp (modified) (3 diffs)
• www/views/rawbioassays/rawdata/view_rawdata.jsp (modified) (2 diffs)
• www/views/rawbioassays/view_rawbioassay.jsp (modified) (3 diffs)

trunk/config/dist/web.xml

@@ -138 +138 @@
     <servlet-name>upload</servlet-name>
     <url-pattern>/filemanager/upload/Upload</url-pattern>
-  </servlet-mapping>
-
-  <!-- The SpotImage servlet used to view spot images in a raw bioassay -->
-  <servlet>
-    <description>Servlet for viewing spot images created from raw bioassay data</description>
-    <display-name>Spot images servlet</display-name>
-    <servlet-name>spotimage</servlet-name>
-    <servlet-class>
-      net.sf.basedb.clients.web.servlet.ViewSpotImage
-    </servlet-class>
-  </servlet>
-  <servlet-mapping>
-    <servlet-name>spotimage</servlet-name>
-    <url-pattern>/views/rawbioassays/rawdata/spotimage/*</url-pattern>
   </servlet-mapping>
 

trunk/www/views/experiments/explorer/view/view.jsp

@@ -70 +70 @@
   import="net.sf.basedb.util.formatter.Formatter"
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
-  import="net.sf.basedb.clients.web.formatter.SpotImageFormatter"
   import="net.sf.basedb.clients.web.taglib.table.TableColumn"
   import="java.util.Date"
@@ -130 +129 @@
   {
     DynamicUtil.addRawDataColumns(spotColumns, dc, rawDataType, "raw.", "$", "[Raw] ");
-    spotColumns.add(new TableColumn("raw.spotimage", "$id", "raw('id')", Type.INT, 
-      "[Raw] Spotimage", "", "auto", false, false, false, null, 
-      new SpotImageFormatter(dc, rawDataType, root)));
   }
 

trunk/www/views/rawbioassays/bioassays.js

@@ -83 +83 @@
       Buttons.addClickHandler('btnShare', Buttons.shareItem, attributes);
       Buttons.addClickHandler('btnSetOwner', Buttons.setOwner, attributes);
-      Buttons.addClickHandler('btnEditSpotImages', bioassays.editSpotImages, attributes);
       Buttons.addClickHandler('btnExport', Buttons.runPlugin, attributes);
       Buttons.addClickHandler('btnImport', Buttons.runPlugin, attributes);
@@ -131 +130 @@
   }
 
-  
-  bioassays.editSpotImages = function()
-  {
-    var url = 'index.jsp?ID='+App.getSessionId();
-    url += '&cmd=EditSpotImages&item_id='+Data.get('page-data', 'item-id');
-    Dialogs.openPopup(url, 'EditSpotImages', 600, 400);
-  }
-
   bioassays.viewRawData = function()
   {

trunk/www/views/rawbioassays/index.jsp

@@ -231 +231 @@
     forward = editPage;
   }
-  else if ("EditSpotImages".equals(cmd))
-  {
-    // Display the spot images edit page for a single item (should be opened in a popup)
-    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
-    redirect = "edit_spotimages.jsp?ID="+ID;
-  }
   else if ("NewItem".equals(cmd))
   {
@@ -585 +579 @@
     redirect = "../../views/itemlists/index.jsp?ID="+ID+"&cmd=NewItem&addItems=1&memberType=RAWBIOASSAY&formId=rawbioassays";
   }
-  else if ("CreateSpotImages".equals(cmd))
-  {
-    dc = sc.newDbControl();
-    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
-    RawBioAssay rba = RawBioAssay.getById(dc, cc.getId());
-    
-    int redFileId = Values.getInt(request.getParameter("redfile_id"));
-    File red = redFileId == 0 ? null : File.getById(dc, redFileId);
-    int greenFileId = Values.getInt(request.getParameter("greenfile_id"));
-    File green = greenFileId == 0 ? null : File.getById(dc, greenFileId);
-    int blueFileId = Values.getInt(request.getParameter("bluefile_id"));
-    File blue = blueFileId == 0 ? null : File.getById(dc, blueFileId);
-
-    String path = Values.getStringOrNull(request.getParameter("path"));
-    if (path.startsWith("~/"))
-    {
-      User user = User.getById(dc, sc.getLoggedInUserId());
-      path = "~"+user.getLogin()+path.substring(1);
-    }
-    Path p = new Path(path, Path.Type.FILE);
-    File saveAs = File.getByPath(dc, p, true);
-    if (saveAs.isInDatabase() && !Values.getBoolean(request.getParameter("overwrite")))
-    {
-      throw new ItemAlreadyExistsException("File[path="+path+"]");
-    }
-    
-    IntegerParameterType integerParameter = new IntegerParameterType();
-    FloatParameterType floatParameter = new FloatParameterType();
-    FileParameterType fileParameter = new FileParameterType();
-    ItemParameterType<RawBioAssay> itemParameter = new ItemParameterType<>(RawBioAssay.class, null);
-    StringParameterType stringParameter = new StringParameterType();
-    BooleanParameterType booleanParameter = new BooleanParameterType();
-    
-    PluginDefinition plugin = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.SpotImageCreator");
-    Job job = Job.getNew(dc, plugin, null, null);
-    job.setName("Create spot images for raw bioassay: " + rba.getName());
-    job.setParameterValue("rawBioAssay", "Raw bioassay", 
-      "The raw bioassay to create spot images for", itemParameter, rba);
-    job.setParameterValue("xScale", "X scale factor", 
-      "The raw data X value will be divided by this value to get the pixel coordinate", 
-      integerParameter, Values.getInt(request.getParameter("x_scale")));
-    job.setParameterValue("yScale", "Y scale factor", 
-      "The raw data Y value will be divided by this value to get the pixel coordinate", 
-      integerParameter, Values.getInt(request.getParameter("y_scale")));
-    job.setParameterValue("xOffset", "X offset value",
-      "The offset is subtracted from the raw data X value",
-      integerParameter, Values.getInt(request.getParameter("x_offset")));
-    job.setParameterValue("yOffset", "Y offset value",
-      "The offset is subtracted from the raw data Y value",
-      integerParameter, Values.getInt(request.getParameter("y_offset")));
-    job.setParameterValue("spotsize", "Spot size", "The size of each spot in pixels",
-      integerParameter, Values.getInt(request.getParameter("spotsize")));
-    job.setParameterValue("gamma", "Gamma", "Gamma correction for display",
-      floatParameter, Values.getFloat(request.getParameter("gamma")));
-    job.setParameterValue("quality", "Quality", 
-      "The quality is a number between 0.0 and 1.0, with 1.0 indicating highest quality.", 
-      floatParameter, Values.getFloat(request.getParameter("quality")));
-    job.setParameterValue("redFile", "Red image", 
-      "The file containing the image to use for the red part", fileParameter, red);
-    job.setParameterValue("greenFile", "Green image", 
-      "The file containing the image to use for the green part", fileParameter, green);
-    job.setParameterValue("blueFile", "Blue image",
-      "The file containing the image to use for the red part", fileParameter, blue);
-    job.setParameterValue("path", "Save as", 
-      "The file name where the spot images should be saved", stringParameter, path);
-    job.setParameterValue("overwrite", "Overwrite", 
-      "If an existing file should be overwritten or not", booleanParameter, Values.getBoolean(request.getParameter("overwrite")));
-    
-    dc.saveItem(job);
-    dc.commit();
-
-    redirect = "../jobs/index.jsp?ID="+ID+"&cmd=ViewItem&item_id="+job.getId();
-  }
   else
   {

trunk/www/views/rawbioassays/rawdata/list_rawdata.jsp

@@ -288 +288 @@
         filterable="true"
         exportable="true"
-      />
-      <tbl:columndef 
-        id="spotImage"
-        title="Spot image"
       />
       <%
@@ -709 +705 @@
           int index = cc.getPage()*cc.getRowsPerPage();
           int selectedItemId = cc.getId();
-          boolean hasSpotImages = rawBioAssay.hasSpotImages();
           if (rawData != null)
           {
@@ -763 +758 @@
                 <tbl:cell column="x"><%=item.getX()%></tbl:cell>
                 <tbl:cell column="y"><%=item.getY()%></tbl:cell>
-                <tbl:cell column="spotImage">
-                  <%
-                  if (hasSpotImages)
-                  {
-                    %>
-                    <img class="spotimage" src="spotimage/<%=ID%>/<%=rawBioAssay.getId()%>/<%=itemId%>/spot<%=item.getPosition()%>.png">
-                    <%
-                  }
-                  %>
-                </tbl:cell>
                 <%
                 for (RawDataProperty rdp : rawBioAssay.getRawDataType().getProperties())

trunk/www/views/rawbioassays/rawdata/view_rawdata.jsp

@@ -79 +79 @@
   final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, rawDataType.getId(), null, null);
   final int itemId = cc.getId();
-  final boolean hasSpotImages = rawBioAssay.hasSpotImages();  
   
   Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
@@ -138 +137 @@
         <th class="leftborder">Feature</th>
         <td><%=feature == null ? "<i>- none -</i>" : feature.getId()%></td>
-      </tr>
-      <tr>
-        <th>Spot image</th>
-        <td>
-          <%
-          if (hasSpotImages)
-          {
-            %>
-            <img class="spotimage" src="spotimage/<%=ID%>/<%=rawBioAssay.getId()%>/<%=itemId%>/spot<%=rawData.getPosition()%>.png">
-            <%
-          }
-          else
-          {
-            %>
-            <i>- none -</i>
-            <%
-          }
-          %>
-        </td>
-        <th class="leftborder"></th>
-        <td></td>
       </tr>
       </tbody>

trunk/www/views/rawbioassays/view_rawbioassay.jsp

@@ -39 +39 @@
   import="net.sf.basedb.core.Experiment"
   import="net.sf.basedb.core.RawDataType"
-  import="net.sf.basedb.core.SpotImages"
   import="net.sf.basedb.core.Protocol"
   import="net.sf.basedb.core.Software"
@@ -268 +267 @@
               tooltip="Run a plugin" 
               visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>"
-            />
-            <tbl:button
-              id="btnEditSpotImages"
-              image="runplugin.png" 
-              title="Create spot images&hellip;"
-              visible="<%=writePermission && rawBioAssay.getNumDbSpots() > 0%>"
             />
             <ext:render extensions="<%=invoker%>" context="<%=jspContext%>" 
@@ -465 +458 @@
           }
         }
-        if (rawBioAssay.hasSpotImages())
-        {
-          SpotImages spi = rawBioAssay.getSpotImages();
-          %>
-          <tbody class="sectionheader">
-            <tr>
-              <th colspan="4">Spot images</th>
-            </tr>
-          </tbody>
-          <tr>
-            <th>X scale</th>
-            <td><%=spi.getXScale()%></td>
-            <th class="leftborder">Spot size</th>
-            <td><%=spi.getSpotsize()%></td>
-          </tr>
-          <tr>
-            <th>Y scale</th>
-            <td><%=spi.getYScale()%></td>
-            <th class="leftborder">Gamma correction</th>
-            <td><%=spi.getGamma()%></td>
-          </tr>
-          <tr>
-            <th>X offset</th>
-            <td><%=spi.getXOffset()%></td>
-            <th class="leftborder">Quality</th>
-            <td><%=spi.getQuality()%></td>
-          </tr>
-          <tr>
-            <th>Y offset</th>
-            <td><%=spi.getYOffset()%></td>
-            <th class="leftborder"></th>
-            <td></td>
-          </tr>
-          <tr>
-            <th class="topborder">Red image file</th>
-            <td colspan="3" class="topborder"><base:propertyvalue item="<%=spi%>" property="redImageFile" /></td>
-          </tr>
-          <tr>
-            <th>Green image file</th>
-            <td colspan="3"><base:propertyvalue item="<%=spi%>" property="greenImageFile" /></td>
-          </tr>
-          <tr>
-            <th>Blue image file</th>
-            <td colspan="3"><base:propertyvalue item="<%=spi%>" property="blueImageFile" /></td>
-          </tr>
-          <tr>
-            <th>Spot images file</th>
-            <td colspan="3"><base:propertyvalue item="<%=spi%>" property="spotImagesFile" /></td>
-          </tr>
-          <%
-        }
         %>
         <tr class="dynamic">